package org.cbioportal.legacy.web;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
import io.swagger.v3.oas.annotations.tags.Tag;
import jakarta.validation.Valid;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import org.apache.commons.lang3.math.NumberUtils;
import org.cbioportal.legacy.model.GeneMolecularData;
import org.cbioportal.legacy.model.NumericGeneMolecularData;
import org.cbioportal.legacy.service.MolecularDataService;
import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException;
import org.cbioportal.legacy.web.config.PublicApiTags;
import org.cbioportal.legacy.web.config.annotation.PublicApi;
import org.cbioportal.legacy.web.parameter.HeaderKeyConstants;
import org.cbioportal.legacy.web.parameter.MolecularDataFilter;
import org.cbioportal.legacy.web.parameter.MolecularDataMultipleStudyFilter;
import org.cbioportal.legacy.web.parameter.Projection;
import org.cbioportal.legacy.web.parameter.SampleMolecularIdentifier;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestAttribute;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

@PublicApi
@RestController()
@RequestMapping("/api")
@Validated
@Tag(name = PublicApiTags.MOLECULAR_DATA, description = " ")
public class MolecularDataController {

  @Autowired private MolecularDataService molecularDataService;

  @PreAuthorize(
      "hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/molecular-profiles/{molecularProfileId}/molecular-data",
      method = RequestMethod.GET,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Get all molecular data in a molecular profile")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(
              array =
                  @ArraySchema(schema = @Schema(implementation = NumericGeneMolecularData.class))))
  public ResponseEntity<List<NumericGeneMolecularData>> getAllMolecularDataInMolecularProfile(
      @Parameter(
              required = true,
              description = "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna")
          @PathVariable
          String molecularProfileId,
      @Parameter(required = true, description = "Sample List ID e.g. acc_tcga_all") @RequestParam
          String sampleListId,
      @Parameter(required = true, description = "Entrez Gene ID e.g. 1") @RequestParam
          Integer entrezGeneId,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection)
      throws MolecularProfileNotFoundException {

    List<NumericGeneMolecularData> result =
        filterNonNumberMolecularData(
            molecularDataService.getMolecularData(
                molecularProfileId, sampleListId, Arrays.asList(entrezGeneId), projection.name()));

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(HeaderKeyConstants.TOTAL_COUNT, String.valueOf(result.size()));
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(result, HttpStatus.OK);
    }
  }

  @PreAuthorize(
      "hasPermission(#molecularProfileId, 'MolecularProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/molecular-profiles/{molecularProfileId}/molecular-data/fetch",
      method = RequestMethod.POST,
      consumes = MediaType.APPLICATION_JSON_VALUE,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Fetch molecular data in a molecular profile")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(
              array =
                  @ArraySchema(schema = @Schema(implementation = NumericGeneMolecularData.class))))
  public ResponseEntity<List<NumericGeneMolecularData>> fetchAllMolecularDataInMolecularProfile(
      @Parameter(
              required = true,
              description = "Molecular Profile ID e.g. acc_tcga_rna_seq_v2_mrna")
          @PathVariable
          String molecularProfileId,
      @Parameter(
              required = true,
              description = "List of Sample IDs/Sample List ID and Entrez Gene IDs")
          @Valid
          @RequestBody
          MolecularDataFilter molecularDataFilter,
      @Parameter(description = "Level of detail of the response")
          @RequestParam(defaultValue = "SUMMARY")
          Projection projection)
      throws MolecularProfileNotFoundException {

    List<NumericGeneMolecularData> result;
    if (molecularDataFilter.getSampleListId() != null) {
      result =
          filterNonNumberMolecularData(
              molecularDataService.getMolecularData(
                  molecularProfileId,
                  molecularDataFilter.getSampleListId(),
                  molecularDataFilter.getEntrezGeneIds(),
                  projection.name()));
    } else {
      result =
          filterNonNumberMolecularData(
              molecularDataService.fetchMolecularData(
                  molecularProfileId,
                  molecularDataFilter.getSampleIds(),
                  molecularDataFilter.getEntrezGeneIds(),
                  projection.name()));
    }

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(HeaderKeyConstants.TOTAL_COUNT, String.valueOf(result.size()));
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(result, HttpStatus.OK);
    }
  }

  @PreAuthorize(
      "hasPermission(#involvedCancerStudies, 'Collection<CancerStudyId>', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/molecular-data/fetch",
      method = RequestMethod.POST,
      consumes = MediaType.APPLICATION_JSON_VALUE,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(description = "Fetch molecular data")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(
              array =
                  @ArraySchema(schema = @Schema(implementation = NumericGeneMolecularData.class))))
  public ResponseEntity<List<NumericGeneMolecularData>>
      fetchMolecularDataInMultipleMolecularProfiles(
          @Parameter(
                  hidden = true) // prevent reference to this attribute in the swagger-ui interface
              @RequestAttribute(required = false, value = "involvedCancerStudies")
              Collection<String> involvedCancerStudies,
          @Parameter(
                  hidden =
                      true) // prevent reference to this attribute in the swagger-ui interface. this
              // attribute is needed for the @PreAuthorize tag above.
              @Valid
              @RequestAttribute(
                  required = false,
                  value = "interceptedMolecularDataMultipleStudyFilter")
              MolecularDataMultipleStudyFilter interceptedMolecularDataMultipleStudyFilter,
          @Parameter(
                  required = true,
                  description =
                      "List of Molecular Profile ID and Sample ID pairs or List of Molecular"
                          + "Profile IDs and Entrez Gene IDs")
              @Valid
              @RequestBody(required = false)
              MolecularDataMultipleStudyFilter molecularDataMultipleStudyFilter,
          @Parameter(description = "Level of detail of the response")
              @RequestParam(defaultValue = "SUMMARY")
              Projection projection) {

    List<NumericGeneMolecularData> result;
    if (interceptedMolecularDataMultipleStudyFilter.getMolecularProfileIds() != null) {
      result =
          filterNonNumberMolecularData(
              molecularDataService.getMolecularDataInMultipleMolecularProfiles(
                  interceptedMolecularDataMultipleStudyFilter.getMolecularProfileIds(),
                  null,
                  interceptedMolecularDataMultipleStudyFilter.getEntrezGeneIds(),
                  projection.name()));
    } else {

      List<String> molecularProfileIds = new ArrayList<>();
      List<String> sampleIds = new ArrayList<>();
      extractMolecularProfileAndSampleIds(
          interceptedMolecularDataMultipleStudyFilter, molecularProfileIds, sampleIds);
      result =
          filterNonNumberMolecularData(
              molecularDataService.getMolecularDataInMultipleMolecularProfiles(
                  molecularProfileIds,
                  sampleIds,
                  interceptedMolecularDataMultipleStudyFilter.getEntrezGeneIds(),
                  projection.name()));
    }

    if (projection == Projection.META) {
      HttpHeaders responseHeaders = new HttpHeaders();
      responseHeaders.add(HeaderKeyConstants.TOTAL_COUNT, String.valueOf(result.size()));
      return new ResponseEntity<>(responseHeaders, HttpStatus.OK);
    } else {
      return new ResponseEntity<>(result, HttpStatus.OK);
    }
  }

  private void extractMolecularProfileAndSampleIds(
      MolecularDataMultipleStudyFilter molecularDataMultipleStudyFilter,
      List<String> molecularProfileIds,
      List<String> sampleIds) {

    for (SampleMolecularIdentifier sampleMolecularIdentifier :
        molecularDataMultipleStudyFilter.getSampleMolecularIdentifiers()) {

      molecularProfileIds.add(sampleMolecularIdentifier.getMolecularProfileId());
      sampleIds.add(sampleMolecularIdentifier.getSampleId());
    }
  }

  private List<NumericGeneMolecularData> filterNonNumberMolecularData(
      List<GeneMolecularData> geneMolecularDataList) {

    List<NumericGeneMolecularData> result = new ArrayList<>();
    geneMolecularDataList.forEach(
        g -> {
          String value = g.getValue();
          if (NumberUtils.isNumber(value)) {
            NumericGeneMolecularData data = new NumericGeneMolecularData();
            data.setEntrezGeneId(g.getEntrezGeneId());
            data.setGene(g.getGene());
            data.setMolecularProfileId(g.getMolecularProfileId());
            data.setPatientId(g.getPatientId());
            data.setSampleId(g.getSampleId());
            data.setStudyId(g.getStudyId());
            data.setValue(new BigDecimal(g.getValue()));
            result.add(data);
          }
        });

    return result;
  }
}
